Look here.
http://www.subsim.com/radioroom/showthread.php?t=110960
with this utility could be possible change some things.
In real life a submarine In shallow an sand bottom for sure could be vissible , but in deep waters could be more difficult.
some reduction can help people with low end cards, also probably IA could take a value from a file, independent from Graphics.
For external views is nice , but useless for people who donīt use external camera, the bad thing is if you disable transparent water you disable fog and other things too.
another game which have a nice transparent water is pirates of the caribbean.